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Volumn 68, Issue 1, 2007, Pages 159-169

Flexible relaxation of rigid-body docking solutions

Author keywords

Flexible docking; Induced fit; Molecular dynamics; Protein interactions; Scoring funtions

Indexed keywords

BARNASE; BARSTAR; BOWMAN BIRK INHIBITOR; CHYMOTRYPSIN A; CHYMOTRYPSIN INHIBITOR; COLICIN; CYCLOPHILIN; EGLIN C; KALLIKREIN; KARYOPHERIN BETA; OVOMUCOID; PROTEIN; RIBONUCLEASE; SUBTILISIN; TRANSFORMING GROWTH FACTOR BETA; TRANSFORMING GROWTH FACTOR BETA RECEPTOR; TRYPSIN; VON WILLEBRAND FACTOR;

EID: 34249884544     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21391     Document Type: Article
Times cited : (41)

References (53)
  • 1
    • 0036421126 scopus 로고    scopus 로고
    • Protein modules and protein-protein interaction
    • Janin J, Wodak SJ. Protein modules and protein-protein interaction. Adv Protein Chem 2002;61:1-8.
    • (2002) Adv Protein Chem , vol.61 , pp. 1-8
    • Janin, J.1    Wodak, S.J.2
  • 3
    • 0345600247 scopus 로고    scopus 로고
    • Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, Li Y, Hao YL, Ooi CE, Godwin B, Vitols E, Vijayadamodar G, Pochart P, Machineni H, Welsh M, Kong Y, Zerhusen B, Malcolm R, Varrone Z, Collis A, Minto M, Burgess S, McDaniel L, Stimpson E, Spriggs F, Williams J, Neurath K, Ioime N, Agee M, Voss E, Furtak K, Renzulli R, Aanensen N, Carrolla S, Bickelhaupt E, Lazovatsky Y, DaSilva A, Zhong J, Stanyon CA, Finley RL, Jr, White KP, Braverman M, Jarvie T, Gold S, Leach M, Knight J, Shimkets RA, McKenna MP, Chant J, Rothberg JM. A protein interaction map of Drosophila melanogaster. Science 2003;302: 1727-1735.
    • Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, Li Y, Hao YL, Ooi CE, Godwin B, Vitols E, Vijayadamodar G, Pochart P, Machineni H, Welsh M, Kong Y, Zerhusen B, Malcolm R, Varrone Z, Collis A, Minto M, Burgess S, McDaniel L, Stimpson E, Spriggs F, Williams J, Neurath K, Ioime N, Agee M, Voss E, Furtak K, Renzulli R, Aanensen N, Carrolla S, Bickelhaupt E, Lazovatsky Y, DaSilva A, Zhong J, Stanyon CA, Finley RL, Jr, White KP, Braverman M, Jarvie T, Gold S, Leach M, Knight J, Shimkets RA, McKenna MP, Chant J, Rothberg JM. A protein interaction map of Drosophila melanogaster. Science 2003;302: 1727-1735.
  • 4
    • 33646472024 scopus 로고    scopus 로고
    • High-resolution protein-protein docking
    • Gray JJ. High-resolution protein-protein docking. Curr Opin Struct Biol 2006;16:183-193.
    • (2006) Curr Opin Struct Biol , vol.16 , pp. 183-193
    • Gray, J.J.1
  • 5
    • 0036468385 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions by docking methods
    • Smith GR, Sternberg MJE. Prediction of protein-protein interactions by docking methods. Curr Opin Struct Biol 2002;12:28-35.
    • (2002) Curr Opin Struct Biol , vol.12 , pp. 28-35
    • Smith, G.R.1    Sternberg, M.J.E.2
  • 6
    • 21644469377 scopus 로고    scopus 로고
    • Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures
    • Méndez R, Leplae R, Lensink MF, Wodak SJ. Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins 2005;60:150-169.
    • (2005) Proteins , vol.60 , pp. 150-169
    • Méndez, R.1    Leplae, R.2    Lensink, M.F.3    Wodak, S.J.4
  • 7
    • 0034212826 scopus 로고    scopus 로고
    • BiGGER: A new (soft) docking algorithm for predicting protein interactions
    • Palma PN, Krippahl L, Wampler JE, Moura JJG. BiGGER: a new (soft) docking algorithm for predicting protein interactions. Proteins 2000;39:372-384.
    • (2000) Proteins , vol.39 , pp. 372-384
    • Palma, P.N.1    Krippahl, L.2    Wampler, J.E.3    Moura, J.J.G.4
  • 8
    • 15244355250 scopus 로고    scopus 로고
    • The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking
    • Smith GR, Sternberg MJE, Bates PA. The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking. J Mol Biol 2005;347:1077-1101.
    • (2005) J Mol Biol , vol.347 , pp. 1077-1101
    • Smith, G.R.1    Sternberg, M.J.E.2    Bates, P.A.3
  • 9
    • 9944237833 scopus 로고    scopus 로고
    • Complementarity of structure ensembles in protein-protein binding
    • Grünberg R, Leckner J, Nilges M. Complementarity of structure ensembles in protein-protein binding. Structure 2004;12:2125-2136.
    • (2004) Structure , vol.12 , pp. 2125-2136
    • Grünberg, R.1    Leckner, J.2    Nilges, M.3
  • 10
    • 0037442962 scopus 로고    scopus 로고
    • HADDOCK: A protein-protein docking approach based on biochemical or biophysical information
    • Dominguez C, Boelens R, Bonvin AMJJ. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc 2003;125:1731-1737.
    • (2003) J Am Chem Soc , vol.125 , pp. 1731-1737
    • Dominguez, C.1    Boelens, R.2    Bonvin, A.M.J.J.3
  • 11
    • 17744364070 scopus 로고    scopus 로고
    • Improved side-chain modeling for protein-protein docking
    • Wang C, Schueler-Furman O, Baker D. Improved side-chain modeling for protein-protein docking. Protein Sci 2005;14:1328-1339.
    • (2005) Protein Sci , vol.14 , pp. 1328-1339
    • Wang, C.1    Schueler-Furman, O.2    Baker, D.3
  • 12
    • 17344380633 scopus 로고    scopus 로고
    • ICM-DISCO docking by global energy optimization with fully flexible side-chains
    • Fernández-Recio J, Totrov M, Abagyan R. ICM-DISCO docking by global energy optimization with fully flexible side-chains. Proteins 2003;52:113-117.
    • (2003) Proteins , vol.52 , pp. 113-117
    • Fernández-Recio, J.1    Totrov, M.2    Abagyan, R.3
  • 13
    • 33644843079 scopus 로고    scopus 로고
    • Accounting for loop flexibility during protein-protein docking
    • Bastard K, Prévost C, Zacharias M. Accounting for loop flexibility during protein-protein docking. Proteins 2006;62:956-969.
    • (2006) Proteins , vol.62 , pp. 956-969
    • Bastard, K.1    Prévost, C.2    Zacharias, M.3
  • 14
    • 29144485503 scopus 로고    scopus 로고
    • Accounting for global protein deformability during protein-protein and protein-ligand docking
    • May A, Zacharias M. Accounting for global protein deformability during protein-protein and protein-ligand docking. Biochim Biophys Acta 2005;1754:225-231.
    • (2005) Biochim Biophys Acta , vol.1754 , pp. 225-231
    • May, A.1    Zacharias, M.2
  • 15
    • 33645961330 scopus 로고    scopus 로고
    • Flexible protein-protein docking
    • Bonvin AM. Flexible protein-protein docking. Curr Opin Struct Biol 2006;16:194-200.
    • (2006) Curr Opin Struct Biol , vol.16 , pp. 194-200
    • Bonvin, A.M.1
  • 16
    • 1842595135 scopus 로고    scopus 로고
    • A novel method for scoring of docked protein complexes using predicted protein-protein binding sites
    • Gottschalk K-E, Neuvirth H, Schreiber G. A novel method for scoring of docked protein complexes using predicted protein-protein binding sites. Protein Eng 2004;17:183-189.
    • (2004) Protein Eng , vol.17 , pp. 183-189
    • Gottschalk, K.-E.1    Neuvirth, H.2    Schreiber, G.3
  • 17
    • 13244277453 scopus 로고    scopus 로고
    • Physicochemical and residue conservation calculations to improve the ranking of protein-protein docking solutions
    • Duan Y, Reddy BVB, Kaznessis YN. Physicochemical and residue conservation calculations to improve the ranking of protein-protein docking solutions. Protein Sci 2005;14:316-328.
    • (2005) Protein Sci , vol.14 , pp. 316-328
    • Duan, Y.1    Reddy, B.V.B.2    Kaznessis, Y.N.3
  • 18
    • 33750014560 scopus 로고    scopus 로고
    • Solvated docking: Introducing water into the modelling of biomolecular complexes
    • van Dijk ADJ, Bonvin AMJJ. Solvated docking: introducing water into the modelling of biomolecular complexes. Bioinformatics 2006;22:2340-2347.
    • (2006) Bioinformatics , vol.22 , pp. 2340-2347
    • van Dijk, A.D.J.1    Bonvin, A.M.J.J.2
  • 19
    • 1542390499 scopus 로고    scopus 로고
    • Identification of protein-protein interaction sites from docking energy landscapes
    • Fernández-Recio J, Totrov M, Abagyan R. Identification of protein-protein interaction sites from docking energy landscapes. J Mol Biol 2004;335:843-865.
    • (2004) J Mol Biol , vol.335 , pp. 843-865
    • Fernández-Recio, J.1    Totrov, M.2    Abagyan, R.3
  • 20
    • 0038161052 scopus 로고    scopus 로고
    • Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
    • Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 2003;331:281-299.
    • (2003) J Mol Biol , vol.331 , pp. 281-299
    • Gray, J.J.1    Moughon, S.2    Wang, C.3    Schueler-Furman, O.4    Kuhlman, B.5    Rohl, C.A.6    Baker, D.7
  • 21
    • 0344980720 scopus 로고    scopus 로고
    • Combination of scoring functions improves discrimination in protein-protein docking
    • Murphy J, Gatchell DW, Prasad JC, Vajda S. Combination of scoring functions improves discrimination in protein-protein docking. Proteins 2003;53:840-854.
    • (2003) Proteins , vol.53 , pp. 840-854
    • Murphy, J.1    Gatchell, D.W.2    Prasad, J.C.3    Vajda, S.4
  • 25
    • 84986512474 scopus 로고    scopus 로고
    • Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 1983;4:187-217.
    • Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 1983;4:187-217.
  • 26
    • 0031565730 scopus 로고    scopus 로고
    • Modelling protein docking using shape complementarity, electrostatics and biochemical information
    • Gabb HA, Jackson RM, Sternberg MJE. Modelling protein docking using shape complementarity, electrostatics and biochemical information. J Mol Biol 1997;272:106-120.
    • (1997) J Mol Biol , vol.272 , pp. 106-120
    • Gabb, H.A.1    Jackson, R.M.2    Sternberg, M.J.E.3
  • 27
    • 34249905541 scopus 로고    scopus 로고
    • http://capri.ebi.ac.uk/round6/Evaluation_20/report.html.
  • 28
    • 0033135638 scopus 로고    scopus 로고
    • Effective energy function for proteins in solution
    • Lazaridis T, Karplus M. Effective energy function for proteins in solution. Proteins 1999;35:133-152.
    • (1999) Proteins , vol.35 , pp. 133-152
    • Lazaridis, T.1    Karplus, M.2
  • 29
    • 0033531959 scopus 로고    scopus 로고
    • Discrimination of the native from misfolded protein models with an energy function including implicit solvation
    • Lazaridis T, Karplus M. Discrimination of the native from misfolded protein models with an energy function including implicit solvation. J Mol Biol 1999;288:477-487.
    • (1999) J Mol Biol , vol.288 , pp. 477-487
    • Lazaridis, T.1    Karplus, M.2
  • 30
    • 0141677983 scopus 로고    scopus 로고
    • Comparison of various implicit solvent models in molecular dynamics simulations of immunoglobulin G light chain dimer
    • Krol M. Comparison of various implicit solvent models in molecular dynamics simulations of immunoglobulin G light chain dimer. J Comput Chem 2003;24:531-546.
    • (2003) J Comput Chem , vol.24 , pp. 531-546
    • Krol, M.1
  • 32
    • 0023475026 scopus 로고
    • Configurational entropy of native proteins
    • Karplus M, Ichiye T, Pettitt B. Configurational entropy of native proteins. Biophys J 1987;52:1083-1085.
    • (1987) Biophys J , vol.52 , pp. 1083-1085
    • Karplus, M.1    Ichiye, T.2    Pettitt, B.3
  • 33
    • 0141956090 scopus 로고    scopus 로고
    • Generalized born model with a simple smoothing function
    • Im W, Lee MS, Brooks CL. Generalized born model with a simple smoothing function. J Comput Chem 2003;24:1691-1702.
    • (2003) J Comput Chem , vol.24 , pp. 1691-1702
    • Im, W.1    Lee, M.S.2    Brooks, C.L.3
  • 34
    • 0001538909 scopus 로고
    • Canonical dynamics: Equilibrium phase-space distributions
    • Hoover WG. Canonical dynamics: equilibrium phase-space distributions. Phys Rev A 1985;31:1695-1697.
    • (1985) Phys Rev A , vol.31 , pp. 1695-1697
    • Hoover, W.G.1
  • 35
    • 34547809547 scopus 로고
    • A unified formulation of the constant temperature molecular dynamics methods
    • Nosé S. A unified formulation of the constant temperature molecular dynamics methods. J Chem Phys 1984;81:511-519.
    • (1984) J Chem Phys , vol.81 , pp. 511-519
    • Nosé, S.1
  • 36
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert J-P, Ciccotti G, Berendsen HJC. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Chem Phys 1977; 23:219-341.
    • (1977) J Chem Phys , vol.23 , pp. 219-341
    • Ryckaert, J.-P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 40
    • 0027166270 scopus 로고
    • Empirical scale of side-chain conformational entropy in protein folding
    • Pickett SD, Sternberg MJE. Empirical scale of side-chain conformational entropy in protein folding. J Mol Biol 1993;231:825-839.
    • (1993) J Mol Biol , vol.231 , pp. 825-839
    • Pickett, S.D.1    Sternberg, M.J.E.2
  • 42
    • 0003742069 scopus 로고
    • London: Department of Biochemistry and Molecular Biology, University College;
    • Hubbard SJ, Thornton JM. NACCESS computer program. London: Department of Biochemistry and Molecular Biology, University College; 1993.
    • (1993) NACCESS computer program
    • Hubbard, S.J.1    Thornton, J.M.2
  • 44
    • 0037422359 scopus 로고    scopus 로고
    • Evaluation of models of electrostatic interactions in proteins
    • Morozov AV, Kortemme T, Baker D. Evaluation of models of electrostatic interactions in proteins. J Phys Chem B 2003;107: 2075-2090.
    • (2003) J Phys Chem B , vol.107 , pp. 2075-2090
    • Morozov, A.V.1    Kortemme, T.2    Baker, D.3
  • 46
    • 0037230970 scopus 로고    scopus 로고
    • Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation
    • Wang T, Wade RC. Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation. Proteins 2003;50:158-169.
    • (2003) Proteins , vol.50 , pp. 158-169
    • Wang, T.1    Wade, R.C.2
  • 47
    • 0035141353 scopus 로고    scopus 로고
    • Dynamical view of the positions of key side chains in protein-protein recognition
    • Kimura R, Brower RC, Vajda S, Camacho CJ. Dynamical view of the positions of key side chains in protein-protein recognition. Biophys J 2001;80:635-642.
    • (2001) Biophys J , vol.80 , pp. 635-642
    • Kimura, R.1    Brower, R.C.2    Vajda, S.3    Camacho, C.J.4
  • 48
    • 0034663658 scopus 로고    scopus 로고
    • Scoring docked conformations generated by rigid-body protein-protein docking
    • Camacho CJ, Gatchell DW, Kimura SR, Vajda S. Scoring docked conformations generated by rigid-body protein-protein docking. Proteins 2000;40:525-537.
    • (2000) Proteins , vol.40 , pp. 525-537
    • Camacho, C.J.1    Gatchell, D.W.2    Kimura, S.R.3    Vajda, S.4
  • 49
    • 0037195144 scopus 로고    scopus 로고
    • A simple physical model for binding energy hot spots in protein-protein complexes
    • Kortemme T, Baker D. A simple physical model for binding energy hot spots in protein-protein complexes. Proc Natl Acad Sci USA 2002;99:14116-14121.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 14116-14121
    • Kortemme, T.1    Baker, D.2
  • 50
    • 31944436020 scopus 로고    scopus 로고
    • Protein design simulations suggest that side-chain conformational entropy is not a strong determinant of amino acid environmental preferences
    • Hu X, Kuhlman B. Protein design simulations suggest that side-chain conformational entropy is not a strong determinant of amino acid environmental preferences. Proteins 2006;62:739-748.
    • (2006) Proteins , vol.62 , pp. 739-748
    • Hu, X.1    Kuhlman, B.2
  • 51
    • 30144445192 scopus 로고    scopus 로고
    • Side-chain entropy effects on protein secondary structure formation
    • Chellgren BW, Creamer TP. Side-chain entropy effects on protein secondary structure formation. Proteins 2006;62:411-420.
    • (2006) Proteins , vol.62 , pp. 411-420
    • Chellgren, B.W.1    Creamer, T.P.2
  • 52
    • 0037470558 scopus 로고    scopus 로고
    • The thermodynamics of protein - protein recognition as characterized by a combination of volumetric and calorimetrie techniques: The binding of turkey ovomucoid third domain to α- chymotrypsin
    • Filfil R, Chalikian TV. The thermodynamics of protein - protein recognition as characterized by a combination of volumetric and calorimetrie techniques: the binding of turkey ovomucoid third domain to α- chymotrypsin. J Mol Biol 2003;326:1271-1288.
    • (2003) J Mol Biol , vol.326 , pp. 1271-1288
    • Filfil, R.1    Chalikian, T.V.2
  • 53
    • 1242270553 scopus 로고    scopus 로고
    • Protein-protein docking: Is the glass half-full or half-empty?
    • Vajda S, Camacho CJ. Protein-protein docking: is the glass half-full or half-empty? Trends Biotechnol 2004;22:110-116.
    • (2004) Trends Biotechnol , vol.22 , pp. 110-116
    • Vajda, S.1    Camacho, C.J.2


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